I. Field of the Invention
Embodiments of this invention are directed generally to biology, medicine, drug discovery, and diagnostics. In particular embodiments the present invention is directed to cyclic peptoid arrays and use thereof.
II. Background
Peptoid (N-substituted oligoglycines) libraries are rich sources of protein ligands. However, the hits that one obtains from library screening experiments against a given protein generally have only a modest affinity for the target (usually low μM KDs). Therefore, it would be desirable to develop peptoid or libraries that provide hits with higher affinity as a starting point for drug development. It seems likely that one reason for the modest affinity of the hits is that peptoids are inherently “floppy” molecules. Assuming that much of the peptoid molecule must “lock in” to a particular conformation upon binding the protein target, this means that the entropic cost of binding will be high, thus limiting the binding affinity. In theory, peptoids or peptoid-like molecules that are stiffer and might closely resemble the bound conformation even in the unbound state would bind with higher affinity.
One way to attempt to limit the conformational flexibility of a peptoid chain would be to cyclize it. By tethering the two ends of the molecule, many conformations available to the linear molecule can no longer be achieved.
Drug-like small molecules (<500 Daltons) generally do not bind well to the relatively shallow surfaces of proteins involved in protein-protein interactions. Thus, in order to develop effective therapeutic agents against these increasingly important targets, it is necessary to develop libraries of compounds able to cover a greater surface area and engage in multiple contacts with the target protein, as well as efficient methods to screen these libraries. With regard to their protein-binding properties, peptides are an attractive class of molecules, but linear peptides have many undesirable features. They are peptidase- and protease-sensitive, relatively cell impermeable and generally form complexes with only modest dissociation constants in the high nM to mid μM range. However, cyclic peptides can exhibit enhanced cell permeability (Rexai et al., 2006a; Rezai et al., 2006b) and are much less sensitive to enzymatic degradation (Satoh et al., 1996). Moreover, it is presumed that the conformational restriction imposed by cyclization may generally afford higher binding affinities, though rigorous proof for this idea is lacking (Udugamasooriya and Spaller, 2008; Martin, 2007). Indeed, many naturally occurring cyclic peptides and depsipeptides have been found to display potent biological activities (Ho et al., 1996; Banerjee et al., 2008; Lech-Maranda et al., 2007; Fouladi, 2006; Hamada and Shioiri, 2005). This interest has led to the development of facile methods for the creation of either synthetic (Joo et al., 2006) or genetically encoded (Scott et al., 1999; Venkatesh et al., 2000) libraries of cyclic peptides as potential sources of drug leads.
A limitation of peptide libraries, cyclic or linear, is that only a relatively small number of building blocks are available. Moreover, although cyclic peptides can be more cell permeable than their linear counterparts, this appears to be dependent on their ability to form intramolecular hydrogen bonds (Rezai et al., 2006b), a property that is likely to vary from compound to compound. Therefore, the inventors became interested in the development of libraries of cyclic peptoids (N-substituted oligoglycines) (Simon et al., 1992; Shin et al., 2007) as potential protein ligands. Large libraries of peptoids with a wide variety of different side chains (Figliozzi et al., 1996; Horn et al., 2004; Alluri et al., 2003) are readily accessible using split and pool methods and efficient protocols with which to screen these libraries for protein binding have been developed (Alluri et al., 2003; Alluri et al., 2006; Xiao et al., 2007; Reddy et al., 2004; Lim et al., 2007; Zuckermann et al., 1994; Udugamasooriya et al., 2008). However, additional methods of producing coded cyclic peptoid arrays and identifying and sequencing cyclic peptoids is needed.